Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_004360.5(CDH1):c.2439+22C>T

CA8130277

259293 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: cae966bb-09fc-42e2-afa9-87358bd5f675
Approved on: 2023-08-08
Published on: 2023-08-08

HGVS expressions

NM_004360.5:c.2439+22C>T
NM_004360.5(CDH1):c.2439+22C>T
NC_000016.10:g.68829819C>T
CM000678.2:g.68829819C>T
NC_000016.9:g.68863722C>T
CM000678.1:g.68863722C>T
NC_000016.8:g.67421223C>T
NG_008021.1:g.97528C>T
ENST00000261769.10:c.2439+22C>T
ENST00000261769.9:c.2439+22C>T
ENST00000422392.6:c.2256+22C>T
ENST00000562118.1:n.657+22C>T
ENST00000562836.5:n.2510+22C>T
ENST00000566510.5:c.*1105+22C>T
ENST00000566612.5:c.*679+22C>T
ENST00000611625.4:c.2502+22C>T
ENST00000612417.4:c.1853+3265C>T
ENST00000621016.4:c.1866-4384C>T
NM_004360.3:c.2439+22C>T
NM_001317184.1:c.2256+22C>T
NM_001317185.1:c.891+22C>T
NM_001317186.1:c.474+22C>T
NM_004360.4:c.2439+22C>T
NM_001317184.2:c.2256+22C>T
NM_001317185.2:c.891+22C>T
NM_001317186.2:c.474+22C>T
More

Benign

Met criteria codes 1
BA1
Not Met criteria codes 25
PP4 PP1 PP3 PP2 PM6 PM2 PM3 PM1 PM4 PM5 PVS1 BS2 BS4 BS3 BS1 BP2 BP3 BP4 BP1 BP5 BP7 PS2 PS4 PS3 PS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen CDH1 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 3.1

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
CDH1 VCEP
The c.2439+22C>T has a frequency of 0.00096 in gnomAD (271 of 280,840), with a maximum subpopulation frequency of 0.01029 (255 of 24,778) in the African population and includes one homozygote (BA1; http://gnomad.broadinstitute.org). To our knowledge, this variant has not been reported in the literature. In summary, this variant meets criteria to be classified as benign based on ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BA1.
Met criteria codes
BA1
This variant has a frequency of 0.00096 in gnomAD (271 of 280,840), with a maximum subpopulation frequency of 0.01029 (255 of 24,778) in the African population, including one homozygote.
Not Met criteria codes
PP4
PP4 does not apply to CDH1.
PP1
To our knowledge, this variant has not been reported in individuals meeting IGCLC criteria for HDGC.
PP3
This variant is not predicted to alter splicing by multiple in silico tools.
PP2
PP2 does not apply to CDH1.
PM6
To our knowledge, this variant has not been reported as de novo.
PM2
This variant has a frequency of 0.00096 in gnomAD (271 of 280,840), with a maximum subpopulation frequency of 0.01029 (255 of 24,778) in the African population, including one homozygote.
PM3
PM3 does not apply to CDH1.
PM1
PM1 does not apply to CDH1.
PM4
PM4 does not apply to this variant.
PM5
PM5 does not apply to CDH1.
PVS1
PVS1 does not apply to this variant.
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
To our knowledge, this variant has not been reported in individuals meeting IGCLC criteria for HDGC.
BS3
To our knowledge, functional studies supporting an alteration in splicing have not been reported for this variant.
BS1
This variant has a frequency of 0.00096 in gnomAD (271 of 280,840), with a maximum subpopulation frequency of 0.01029 (255 of 24,778) in the African population, including one homozygote.
BP2
To our knowledge, this variant has not been reported in cis or trans with a pathogenic variant.
BP3
BP3 does not apply to CDH1.
BP4
This variant is not predicted to alter splicing by multiple in silico tools.
BP1
BP1 does not apply to CDH1.
BP5
To our knowledge, this variant has not been observed in a case with an alternate molecular basis for disease.
BP7
BP7 does not apply to this variant.
PS2
To our knowledge, this variant has not been reported as de novo.
PS4
To our knowledge, this variant has not been reported in individuals meeting IGCLC criteria for HDGC.
PS3
To our knowledge, functional studies supporting an alteration in splicing have not been reported for this variant.
PS1
PS1 does not apply to this variant.
Curation History
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